Proteins which run high on SDS-PAGE

[RHODES at UCONNVM.UCONN.EDU]

On Tue, 14 May 1996 18:54:58 -0500 Achim said:
>The average protein binds 1.4g SDS/g protein. The charge of
>the high number of SDS molecules bound to the protein should
>more than outnumber any intrinsic charge(s) of
>the protein.
Yes/no - - if you calculate a MOLE ratio, using an average
aa residue MW of 110-120, and calculate the number of SDS
bound PER RESIDUE, it comes out to about 0.5.  Thus, I maintain
that
(a) if P doesn't bind SDS, then one may have anomalously
larger-running proteins, EVEN if the frictional coefficient is
reduced by the kink;
(b) especially for small proteins, there may, be discernible
effects due to amino acid intrinsic charge, but I agree that
the contribution is USUALLY small;
(c) nobody has yet demonstrated to me that the f of a kinked
molecule should be greater than that of a non-kinked equivalent
(which was my original point).

>... high temperatures in the presence of SDS;
are to denature the protein, not to create some sort of high
binding stoichiometry intermediate.
>...diminish the number of SDS-molecules bound.
certainly possible - it might be an interesting study, if it
hasn't already been done, to look at polyP SDS binding and/or
SDS binding as a function of P content.

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